Scoring matrix of 3 sequence alignment
Entering edit mode
7.9 years ago
mhasa006 ▴ 70

I want to perform global sequence alignment on 3 DNA sequences. Now while making the scoring matrix for the dynamic programming, there are 7 possible cases. In case of 2 DNA sequences, the options are either a match or a insert or delete. But in 3 sequence alignment, there are all three match, two match and a gap and two gaps.

Is the following observation of mine is right?

  1. For exact match in three sequence I just add the matching score in the scoring matrix
  2. For two match and a gap I added (matched scored + gap) (i.e. matched score = 2, gap = -2)
  3. For two gaps I added (gap * 2) in the scoring matrix.

Is these observation correct?

sequencing multiple-sequencing • 2.4k views

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